It seems we have a $wgOldChangeTagsIndex global to select between old and new indexes.
Based on our current site config, few wikis have it set to false for them, but this seems to be rather out of date as I found dberrors from outreachwiki in relation to it. I suspect most "newer" wikis would need this set to false
'wgOldChangeTagsIndex' => array(
'default' => true, // For compat with index on changetags table
'flaggedrevs_labswikimedia' => false, -Aaron 4-21-2010
'fawikinews' => false, Strangely, this one has the new index names --catrope Oct 27 2010
'outreachwiki' => false,
It'd be nice if we could get production cleaned up, and then remove this damn global.
maintenance/archives/patch-change_tag-indexes.sql is the patch to run